Problem in Windows 7

I've spent 2 days trying to solve this problem. I have a legacy application that writes to the Registry.
If I run it from the C:\My folder\LEGACY.EXE it runs fine.
but if I run it from C:\PROGRAM FILES\APPLICATION\LEGACY.EXE, it does not work.
What difference is there between running it from the c:\ vs the c:\Program Files

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